GeneBe

rs55659625

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001002860.4(BTBD7):​c.2122-17_2122-13delTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,208,008 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000025 ( 0 hom. )

Consequence

BTBD7
NM_001002860.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.08
Variant links:
Genes affected
BTBD7 (HGNC:18269): (BTB domain containing 7) Predicted to be involved in regulation of branching involved in salivary gland morphogenesis. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BTBD7NM_001002860.4 linkc.2122-17_2122-13delTTTTT intron_variant Intron 9 of 10 ENST00000334746.10 NP_001002860.2 Q9P203-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BTBD7ENST00000334746.10 linkc.2122-17_2122-13delTTTTT intron_variant Intron 9 of 10 1 NM_001002860.4 ENSP00000335615.5 Q9P203-1
BTBD7ENST00000554565.5 linkc.1069-17_1069-13delTTTTT intron_variant Intron 7 of 8 1 ENSP00000451010.1 Q9P203-5
BTBD7ENST00000553975.1 linkc.967-17_967-13delTTTTT intron_variant Intron 5 of 6 2 ENSP00000450778.1 H0YJ41
BTBD7ENST00000355125.3 linkn.*743-17_*743-13delTTTTT intron_variant Intron 6 of 7 2 ENSP00000347246.3 H3BLV3

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000248
AC:
3
AN:
1208008
Hom.:
0
AF XY:
0.00000171
AC XY:
1
AN XY:
586114
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000214
Gnomad4 FIN exome
AF:
0.0000247
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000202
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-93712644; API